Thank you both very much for your help. One last question: Ilyas, what did
you use to process the .pdb file? Did you also use the H++ program (
http://biophysics.cs.vt.edu/H++/ ) Marek used?
Audrey
On Thu, Mar 17, 2011 at 12:59 PM, Ilyas Yildirim <
i-yildirim.northwestern.edu> wrote:
> Melanie -
>
> I tested both structures and leap could create the prmtop/inpcrd files.
> There are close contact problems printed out in leap, which you can
> disregard. Those close contact problems can be solved after doing
> minimization on the structure.
>
> I would not directly use a .pdb file downloaded from pdb.org. I would
> first post-process it before loading it to leap. In your case, for some
> reason which I dont know, leap does not understand the structure. Look at
> the attached tmp.pdb file, which is the processed version of 3NJW pdb file.
> Using this .pdb will create prmtop/inpcrd.
>
> Also, do you need water molecules from the .pdb file? If not, remove them
> before creating the prmtop/inpcrd files.
>
> Good luck,
>
>
> Ilyas Yildirim, Ph.D.
> -----------------------------------------------------------
> = Department of Chemistry - 2145 Sheridan Road =
> = Northwestern University - Evanston, IL 60208 =
> = Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
> = http://www.pas.rochester.edu/~yildirim/ =
> -----------------------------------------------------------
>
>
> On Thu, 17 Mar 2011, Melanie wrote:
>
> Hi Ilyas,
>> This should be a regular system. I am using a structure from the PDB; I
>> have
>> attached it. As a background, I edited 3NJW_old to 3NJW by changing the
>> CYS
>> to CYX, since the structure contains a cysteine disulfide bond. This edit
>> fixed some of the original errors I had regarding that particular bond.
>> If I were to treat this as a regular system, how would I change the
>> structure? And if I have to define my own residue library, would I be
>> using
>> the addPdbResMap function or something else?
>>
>> Thanks very much,
>> Melanie
>>
>> On Tue, Mar 15, 2011 at 11:18 AM, Ilyas Yildirim <
>> i-yildirim.northwestern.edu> wrote:
>>
>> Melanie - It seems that you have a system where you have a bond (in the
>>> atom type notation) N3-C. I checked out parm99.dat and there is not any
>>> such bond defined. As a result, you need to defined those missing
>>> parameters. Is this a regular system or do you have your own residue
>>> library defined, which you want to use in this particular system?
>>>
>>> Ilyas Yildirim, Ph.D.
>>> -----------------------------------------------------------
>>> = Department of Chemistry - 2145 Sheridan Road =
>>> = Northwestern University - Evanston, IL 60208 =
>>> = Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
>>> = http://www.pas.rochester.edu/~yildirim/ =
>>> -----------------------------------------------------------
>>>
>>>
>>> On Tue, 15 Mar 2011, Melanie wrote:
>>>
>>> Hi all,
>>>> I've been trying to figure out what is wrong with my molecule. This set
>>>>
>>> of
>>>
>>>> missing parameters appears to be stemming from one particular bond or
>>>>
>>> area.
>>>
>>>> When leap would not save my parameter files because of these errors, I
>>>>
>>> tried
>>>
>>>> to figure out which parameters I was missing by using parmchk and
>>>> antechamber; unfortunately, both of these also ended with an error
>>>>
>>> message.
>>>
>>>> I also tried addIons, to no avail. Can someone please tell me how to fix
>>>> this, and also *how to detect certain basic errors that may cause a
>>>> parameter file to not be saved*, etc.
>>>> I have pasted the missing parameters error and antechamber errors below,
>>>>
>>> as
>>>
>>>> well as attached the leap.log file.
>>>>
>>>> *> saveamberparm njw njw.prmtop njw.inpcrd*
>>>> *Checking Unit.*
>>>> *WARNING: The unperturbed charge of the unit: -1.000000 is not zero.*
>>>> *
>>>> *
>>>> * -- ignoring the warning.*
>>>> *
>>>> *
>>>> *Building topology.*
>>>> *Building atom parameters.*
>>>> *Building bond parameters.*
>>>> *Could not find bond parameter for: N3 - C*
>>>> *Building angle parameters.*
>>>> *Could not find angle parameter: CT - N3 - C*
>>>> *Could not find angle parameter: H - N3 - C*
>>>> *Could not find angle parameter: H - N3 - C*
>>>> *Could not find angle parameter: H - N3 - C*
>>>> *Could not find angle parameter: N3 - C - CT*
>>>> *Could not find angle parameter: N3 - C - O2*
>>>> *Could not find angle parameter: N3 - C - O2*
>>>> *Building proper torsion parameters.*
>>>> * ** No torsion terms for CT-N3-C-CT*
>>>> * ** No torsion terms for CT-N3-C-O2*
>>>> * ** No torsion terms for CT-N3-C-O2*
>>>> * ** No torsion terms for H-N3-C-CT*
>>>> * ** No torsion terms for H-N3-C-O2*
>>>> * ** No torsion terms for H-N3-C-O2*
>>>> * ** No torsion terms for H-N3-C-CT*
>>>> * ** No torsion terms for H-N3-C-O2*
>>>> * ** No torsion terms for H-N3-C-O2*
>>>> * ** No torsion terms for H-N3-C-CT*
>>>> * ** No torsion terms for H-N3-C-O2*
>>>> * ** No torsion terms for H-N3-C-O2*
>>>> *Building improper torsion parameters.*
>>>> * ** Warning: No sp2 improper torsion term for C*-CN-CB-CA*
>>>> * atoms are: CG CE2 CD2 CE3*
>>>> * ** Warning: No sp2 improper torsion term for NA-CA-CN-CB*
>>>> * atoms are: NE1 CZ2 CE2 CD2*
>>>> * ** Warning: No sp2 improper torsion term for CT-O2-C-N3*
>>>> * atoms are: CB OD1 CG N*
>>>> * ** Warning: No sp2 improper torsion term for CT-O2-C-N3*
>>>> * atoms are: CB OD2 CG N*
>>>> * ** Warning: No sp2 improper torsion term for C*-CN-CB-CA*
>>>> * atoms are: CG CE2 CD2 CE3*
>>>> * ** Warning: No sp2 improper torsion term for NA-CA-CN-CB*
>>>> * atoms are: NE1 CZ2 CE2 CD2*
>>>> * ** Warning: No sp2 improper torsion term for C*-CN-CB-CA*
>>>> * atoms are: CG CE2 CD2 CE3*
>>>> * ** Warning: No sp2 improper torsion term for NA-CA-CN-CB*
>>>> * atoms are: NE1 CZ2 CE2 CD2*
>>>> * total 62 improper torsions applied*
>>>> *Building H-Bond parameters.*
>>>> *Parameter file was not saved.*
>>>>
>>>> --------------------------
>>>>
>>>> *[.login2 ~]$ $AMBERHOME/exe/antechamber -i
>>>>
>>> /u/home/campus/template/3NJW.pdb
>>>
>>>> -fi pdb -o njw.prepin -fo prepi -c bcc -s 2*
>>>> *Running: /u/home2/ppk/amber10/bin/bondtype -j full -i
>>>> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac*
>>>> *sh: /u/home2/ppk/amber10/bin/bondtype: Permission denied*
>>>> *Error: cannot run "/u/home2/ppk/amber10/bin/bondtype -j full -i
>>>> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
>>>> judgebondtype() of antechamber.c properly, exit*
>>>>
>>>>
>>>>
>>>> Thank you,
>>>> Melanie
>>>>
>>>>
>>> _______________________________________________
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>
>>
>> --
>> ********
>> Minnie
>> ********
>>
>
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Received on Fri Mar 18 2011 - 21:30:02 PDT
